Publications

For a complete chronological ordering of my publications please see my google scholar profile here

On this page I have listed papers based on when I worked on them/career stage, so they are not necessarily chronological.

Italics denotes a mentored undergraduate.

*asterisks denotes equal contribution

Have one I’m finishing the edits for regarding data analysis and gene tree conflict, stay tuned!

Putting the final touches on a couple in prep, some Ericales work, edge-based analyses, and work on within gene conflict. Coming soon!

SA Smith, N Walker-Hale, JF Walker and JW Brown. Nested phylogenetic conflicts, combinability, and deep phylogenomics in plants. In press. Systematic Biology.

SA Smith and JF Walker. PyPHLAWD: A python package for phylogenetic dataset construction (2019). Methods in Ecology and Evolution.

N Wang, Y Yang, MJ Moore, SF Brockington, JF Walker, JW Brown, T Feng, A Timoneda, C Edwards, L Majure, R Puente, U Eggli, B Liang and SA Smith. Evolution of Portulacineae marked by adaptation to harsh environments, gene tree conflict, and gene family expansion (2019). Molecular Biology and Evolution.

JF Walker, JW Brown and SA Smith. Analyzing contentious relationships and outlier genes in phylogenomics (2018). Systematic Biology, 67:5.

JF Walker, Y Yang, T Feng, A Timoneda, J Mikenas, V Hutchison, C Edwards, N Wang, S Ahluwalia, J Olivieri, N Walker-Hale, LC Majure, R Puente, G Kadereit, M Lauterbach, U Eggli, H Flores-Olvera, H Ochoterena, SF Brockington, MJ Moore and SA Smith. From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provides further insight to the evolution of Caryophyllales (2018). American Journal of Botany, 105:3.

JB Pease, JW Brown, JF Walker, CE Hinchliff and SA Smith. Quartet sampling distinguishes lack of support from conflicting support in plant tree of life (2018). American Journal of Botany, 105:3.

SA Smith, JW Brown, Y Yang, R Bruenn, CP Drummond, SF Brockington, JF Walker, N Last, NA Douglas and MJ Moore. Disparity, Diversity, and Duplications in the Caryophyllales (2018). New Phytologist, 217:2.

JF Walker, Y Yang, MJ Moore, J Mikenas, SF Brockington, A Timoneda and SA Smith. Widespread paleopolyploidy, gene tree conflict and recalcitrant relationships among the carnivorous Caryophyllales (2017). American Journal of Botany, 104:6.

JW Brown*, JF Walker* and SA Smith (2017). Phyx: Phylogenetic tools for Unix. Bioinformatics, 33:12.

Y Yang, MJ Moore, SF Brockington, A Timoneda, T Feng, H Marx, JF Walker and SA Smith (2017). An efficient field and laboratory workflow for plant phylotranscriptomic projects. Applications in Plant Sciences, 5:3.

JF Walker, RK Jansen, MJ Zanis and NC Emery (2015). Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes. American Journal of Botany, 102:11.